X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=5ddaa5e20849e5fb14df7adff77fc78a6a7d803e;hb=f13833b55dc6e05e5630b8dc465059a5cd2848a8;hp=cb17e64797746f17d9ed1cabf8e1e7ccba7526c4;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index cb17e64..5ddaa5e 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,332 +1,376 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationLabels
-    extends Panel implements ActionListener, MouseListener, MouseMotionListener
-{
-  Image image;
-  boolean active = false;
-  AlignmentPanel ap;
-  AlignViewport av;
-  boolean resizing = false;
-  int oldY, mouseX;
-  static String EDITNAME = "Edit label/description";
-  static String HIDE = "Hide this row";
-  static String DELETE = "Delete this row";
-  static String SHOWALL = "Show all hidden rows";
-  static String OUTPUT_TEXT = "Show Values In Textbox";
-  static String COPYCONS_SEQ = "Copy Consensus Sequence";
-
-  int selectedRow = 0;
-  int scrollOffset = 0;
-
-  Tooltip tooltip;
-
-  public AnnotationLabels(AlignmentPanel ap)
-  {
-    this.ap = ap;
-    this.av = ap.av;
-    setLayout(null);
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public AnnotationLabels(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void setScrollOffset(int y)
-  {
-    scrollOffset = y;
-    repaint();
-  }
-
-  void getSelectedRow(int y)
-  {
-    selectedRow = -1;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    if (aa == null)
-    {
-      return;
-    }
-
-    int height = 0;
-    for (int i = 0; i < aa.length; i++)
-    {
-      if (!aa[i].visible)
-      {
-        continue;
-      }
-
-      height += aa[i].height;
-      if (y < height)
-      {
-        selectedRow = i;
-        break;
-      }
-    }
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-    if (evt.getActionCommand().equals(EDITNAME))
-    {
-      EditNameDialog dialog = new EditNameDialog(
-          aa[selectedRow].label,
-          aa[selectedRow].description,
-          "       Annotation Label",
-          "Annotation Description",
-          ap,
-          "Edit Annotation Name / Description");
-
-      if (dialog.accept)
-      {
-        aa[selectedRow].label = dialog.getName();
-        aa[selectedRow].description = dialog.getDescription();
-        repaint();
-      }
-    }
-    if (evt.getActionCommand().equals(HIDE))
-    {
-      aa[selectedRow].visible = false;
-    }
-    else if (evt.getActionCommand().equals(SHOWALL))
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        aa[i].visible = true;
-      }
-    }
-    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
-      Frame frame = new Frame();
-      frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-                                       ap.alignFrame.getTitle() + " - " +
-                                       aa[selectedRow].label, 500, 100);
-      cap.setText(aa[selectedRow].toString());
-    }
-    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
-    {
-      SequenceI cons = av.getConsensusSeq();
-      if (cons != null)
-      {
-        copy_annotseqtoclipboard(cons);
-      }
-
-    }
-    ap.annotationPanel.adjustPanelHeight();
-    setSize(getSize().width, ap.annotationPanel.getSize().height);
-    ap.validate();
-    ap.paintAlignment(true);
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {
-    getSelectedRow(evt.getY() - scrollOffset);
-
-    if (selectedRow > -1)
-    {
-      if (tooltip == null)
-      {
-        tooltip = new Tooltip(ap.av.alignment.
-                              getAlignmentAnnotation()[selectedRow].
-                              description,
-                              this);
-      }
-      else
-      {
-        tooltip.setTip(ap.av.alignment.
-                       getAlignmentAnnotation()[selectedRow].description);
-      }
-    }
-    else if (tooltip != null)
-    {
-      tooltip.setTip("");
-    }
-
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseReleased(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-    PopupMenu pop = new PopupMenu("Annotations");
-
-    MenuItem item = new MenuItem(EDITNAME);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new MenuItem(HIDE);
-    item.addActionListener(this);
-    pop.add(item);
-    item = new MenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
-    this.add(pop);
-    item = new MenuItem(OUTPUT_TEXT);
-    item.addActionListener(this);
-    pop.add(item);
-
-    if (aa[selectedRow] == ap.av.consensus)
-    {
-      pop.addSeparator();
-      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-          "Ignore Gaps In Consensus",
-          ap.av.getIgnoreGapsConsensus());
-
-      cbmi.addItemListener(new ItemListener()
-      {
-        public void itemStateChanged(ItemEvent e)
-        {
-          ap.av.setIgnoreGapsConsensus(cbmi.getState());
-          ap.paintAlignment(true);
-        }
-      });
-      pop.add(cbmi);
-      final MenuItem cpcons = new MenuItem(COPYCONS_SEQ);
-      cpcons.addActionListener(this);
-      pop.add(cpcons);
-    }
-
-    pop.show(this, evt.getX(), evt.getY());
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void copy_annotseqtoclipboard(SequenceI sq)
-  {
-    if (sq == null || sq.getLength() < 1)
-    {
-      return;
-    }
-    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
-        sq.getStart() + "\t" +
-        sq.getEnd() + "\t" +
-        sq.getSequenceAsString() + "\n");
-    if (av.hasHiddenColumns)
-    {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
-      {
-        int[] region = (int[])
-            av.getColumnSelection().getHiddenColumns().elementAt(i);
-
-        jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]
-            {region[0],
-            region[1]});
-      }
-    }
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    int w = getSize().width;
-    if (image == null || w != image.getWidth(this))
-    {
-      image = createImage(w, ap.annotationPanel.getSize().height);
-    }
-
-    drawComponent(image.getGraphics(), w);
-    g.drawImage(image, 0, 0, this);
-  }
-
-  public void drawComponent(Graphics g, int width)
-  {
-    g.setFont(av.getFont());
-    FontMetrics fm = g.getFontMetrics(av.getFont());
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getSize().width, getSize().height);
-
-    g.translate(0, scrollOffset);
-    g.setColor(Color.black);
-
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
-
-    if (aa != null)
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
-        {
-          continue;
-        }
-
-        x = width - fm.stringWidth(aa[i].label) - 3;
-
-        if (aa[i].graph > 0)
-        {
-          y += (aa[i].height / 3);
-        }
-
-        g.drawString(aa[i].label, x, y);
-
-        if (aa[i].graph > 0)
-        {
-          y += (2 * aa[i].height / 3);
-        }
-        else
-        {
-          y += aa[i].height;
-        }
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class AnnotationLabels
+    extends Panel implements ActionListener, MouseListener, MouseMotionListener
+{
+  Image image;
+  boolean active = false;
+  AlignmentPanel ap;
+  AlignViewport av;
+  boolean resizing = false;
+  int oldY, mouseX;
+
+  static String ADDNEW = "Add New Row";
+  static String EDITNAME = "Edit Label/Description";
+  static String HIDE = "Hide This Row";
+  static String SHOWALL = "Show All Hidden Rows";
+  static String OUTPUT_TEXT = "Show Values In Textbox";
+  static String COPYCONS_SEQ = "Copy Consensus Sequence";
+
+  int scrollOffset = 0;
+  int selectedRow = -1;
+
+  Tooltip tooltip;
+
+  public AnnotationLabels(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    this.av = ap.av;
+    setLayout(null);
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  public AnnotationLabels(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public void setScrollOffset(int y)
+  {
+    scrollOffset = y;
+    repaint();
+  }
+
+  int getSelectedRow(int y)
+  {
+    int row = -1;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if (aa == null)
+    {
+      return row;
+    }
+
+    int height = 0;
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (!aa[i].visible)
+      {
+        continue;
+      }
+
+      height += aa[i].height;
+      if (y < height)
+      {
+        row = i;
+        break;
+      }
+    }
+
+    return row;
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+    if (evt.getActionCommand().equals(ADDNEW))
+    {
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation("",
+          null,
+          new Annotation[ap.av.alignment.getWidth()]);
+
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
+
+      ap.av.alignment.addAnnotation(newAnnotation);
+      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+    }
+    else if (evt.getActionCommand().equals(EDITNAME))
+    {
+      editLabelDescription(aa[selectedRow]);
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        aa[i].visible = (aa[i].annotations==null) ? false : true;
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       ap.alignFrame.getTitle() + " - " +
+                                       aa[selectedRow].label, 500, 100);
+      cap.setText(aa[selectedRow].toString());
+    }
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+    {
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
+      {
+        copy_annotseqtoclipboard(cons);
+      }
+
+    }
+    ap.annotationPanel.adjustPanelHeight();
+    setSize(getSize().width, ap.annotationPanel.getSize().height);
+    ap.validate();
+    ap.paintAlignment(true);
+  }
+
+  boolean editLabelDescription(AlignmentAnnotation annotation)
+  {
+    Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+                                    +ap.av.getGapCharacter()+"\"",
+                                    annotation.padGaps);
+
+    EditNameDialog dialog = new EditNameDialog(
+        annotation.label,
+        annotation.description,
+        "      Annotation Label",
+        "Annotation Description",
+        ap.alignFrame,
+        "Edit Annotation Name / Description",
+        500, 180, false);
+
+    Panel empty = new Panel(new FlowLayout());
+    empty.add(padGaps);
+    dialog.add(empty);
+    dialog.pack();
+
+    dialog.setVisible(true);
+
+    if (dialog.accept)
+    {
+      annotation.label = dialog.getName();
+      annotation.description = dialog.getDescription();
+      annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
+      repaint();
+      return true;
+    }
+    else
+      return false;
+
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    int row = getSelectedRow(evt.getY() - scrollOffset);
+
+    if (row > -1)
+    {
+      if (tooltip == null)
+      {
+        tooltip = new Tooltip(ap.av.alignment.
+                              getAlignmentAnnotation()[row].
+                              description,
+                              this);
+      }
+      else
+      {
+        tooltip.setTip(ap.av.alignment.
+                       getAlignmentAnnotation()[row].description);
+      }
+    }
+    else if (tooltip != null)
+    {
+      tooltip.setTip("");
+    }
+
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseReleased(MouseEvent evt)
+  {}
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
+  public void mousePressed(MouseEvent evt)
+  {
+    selectedRow = getSelectedRow(evt.getY() - scrollOffset);
+
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    PopupMenu popup = new PopupMenu("Annotations");
+
+    MenuItem item = new MenuItem(ADDNEW);
+    item.addActionListener(this);
+    popup.add(item);
+    item = new MenuItem(EDITNAME);
+    item.addActionListener(this);
+    popup.add(item);
+    item = new MenuItem(HIDE);
+    item.addActionListener(this);
+    popup.add(item);
+    item = new MenuItem(SHOWALL);
+    item.addActionListener(this);
+    popup.add(item);
+    this.add(popup);
+    item = new MenuItem(OUTPUT_TEXT);
+    item.addActionListener(this);
+    popup.add(item);
+
+    if (aa[selectedRow] == ap.av.consensus)
+    {
+      popup.addSeparator();
+      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+          "Ignore Gaps In Consensus",
+          ap.av.getIgnoreGapsConsensus());
+
+      cbmi.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          ap.av.setIgnoreGapsConsensus(cbmi.getState());
+          ap.paintAlignment(true);
+        }
+      });
+      popup.add(cbmi);
+      item = new MenuItem(COPYCONS_SEQ);
+      item.addActionListener(this);
+      popup.add(item);
+    }
+
+    popup.show(this, evt.getX(), evt.getY());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    if (sq == null || sq.getLength() < 1)
+    {
+      return;
+    }
+    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
+        sq.getStart() + "\t" +
+        sq.getEnd() + "\t" +
+        sq.getSequenceAsString() + "\n");
+    if (av.hasHiddenColumns)
+    {
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      {
+        int[] region = (int[])
+            av.getColumnSelection().getHiddenColumns().elementAt(i);
+
+        jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]
+            {region[0],
+            region[1]});
+      }
+    }
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    int w = getSize().width;
+    if (image == null || w != image.getWidth(this))
+    {
+      image = createImage(w, ap.annotationPanel.getSize().height);
+    }
+
+    drawComponent(image.getGraphics(), w);
+    g.drawImage(image, 0, 0, this);
+  }
+
+  public void drawComponent(Graphics g, int width)
+  {
+    g.setFont(av.getFont());
+    FontMetrics fm = g.getFontMetrics(av.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
+
+    g.translate(0, scrollOffset);
+    g.setColor(Color.black);
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    int y = g.getFont().getSize();
+    int x = 0;
+
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+        x = width - fm.stringWidth(aa[i].label) - 3;
+
+        if (aa[i].graph > 0)
+        {
+          y += (aa[i].height / 3);
+        }
+
+        g.drawString(aa[i].label, x, y);
+
+        if (aa[i].graph > 0)
+        {
+          y += (2 * aa[i].height / 3);
+        }
+        else
+        {
+          y += aa[i].height;
+        }
+      }
+    }
+  }
+
+}